I don't know of any court cases or other precedent, no. I am working with the definitions of "software" and "program" as I am familiar with them being used in various software licenses. But that doesn't really matter because the only assumptions I'm basing this argument on are contained in the MIT/Expat and what connectFree has done with Zen.

For the sake of the argument, let's grant you the premise that each file is its own "software" (as the word is used in the MIT/Expat). The only requirement of the license is this: "The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software." So even if connectFree removed all the copyright notices in the source code files, they still meet that condition because the original Zig license is included in their modified copy of Zig. It doesn't matter what the definition of "software" is here, because they meet the conditions regardless of what that definition is.